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Getting started with MaMuT

49 bytes removed, 10:55, 13 March 2017
Saving to a MaMuT file.
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The essential difference with plain TrackMate files is that the files generated by MaMuT have a <tt style="font-size: 1.25em;">Settings</tt> part that points to a BigDataViewer file as image source. Otherwise, the annotation stored in the <tt style="font-size: 1.25em;">Model</tt> section is described in the exact same way. So if you have a script that can load and analyse a TrackMate file, it is likely that it will also work with MaMuT.
In the last <tt style="font-size: 1.25em;">GUIState</tt> section, MaMuT stores several display settings. This is where you will find the brightness settings and the bookmarks location that we imported from the BigDataViewer settings when we launched the new MaMuT annotation and that you may modify later. From now on, they will be stored and retrieve directly from the MaMuT file, so the BigDataViewer settings file we used to launch the annotation is not used anymore.
So after saving, a MaMuT annotation is made of three files. In the case of the demo dataset:
\begin{myitemize} \item * <tt style="font-size: 1.25em;">MaMuT_Parhyale_demo.h5</tt>: this is typically a very large file that contains the raw image data. \item * <tt style="font-size: 1.25em;">MaMuT_Parhyale_demo.xml</tt>: this is the BigDataViewer file. It is a XML file that lists where is the image data and how the possibly several views are arranged in space. This file can be opened in the BigDataViewer, and this is the one you open when you launch a new MaMuT annotation \item * <tt style="font-size: 1.25em;">MaMuT_Parhyale_demo-mamut.xml</tt>: this is the MaMuT file. It contains as we said the the annotation and pointers to the image file.\end{myitemize}
From now on, we will only be interacting with the MaMuT file in MaMuT, but these three files need to travel together.
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